The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.

In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned.

Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

A method has been devised for the electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets. The method results in quantitative transfer of ribosomal proteins from gels containing urea. For sodium dodecyl sulfate gels, the original band pattern was obtained with no loss of resolution, but the transfer was not quantitative. The method allows detection of proteins by autoradiography and is simpler than conventional procedures. The immobilized proteins were detectable by immunological procedures.

Polymerase DNA Directed Gamma 1 (POLg1) Antibody
abx129163-1ml	Abbexa	1 ml	EUR 750

Polymerase DNA Directed Gamma 1 (POLg1) Antibody
abx129163-200l	Abbexa	200 µl	EUR 337.5

Polymerase DNA Directed Gamma 1 (POLg1) Antibody
abx174136-100l	Abbexa	100 µl	EUR 787.5

Polymerase DNA Directed Gamma 1 (POLg1) Antibody
20-abx174136	Abbexa	Ask for price Ask for price	200 ug 1 mg

Polymerase DNA Directed Gamma 1 (POLg1) Antibody
abx174136-1ml	Abbexa	1 ml	Ask for price

Polymerase DNA Directed Gamma 1 (POLg1) Antibody
abx174136-200l	Abbexa	200 µl	Ask for price

Polymerase DNA Directed Gamma 1 (POLG1) Antibody
20-abx217848	Abbexa	Ask for price Ask for price	50 ug 100 ug

Rabbit Polyclonal antibody to DNA polymerase gamma (polymerase (DNA directed), gamma)
TA308753	Origene Technologies GmbH	100 µl	Ask for price

Cat Polymerase DNA Directed Gamma 1 ELISA Kit
MBS086004-INQUIRE	MyBiosource	INQUIRE	Ask for price

Rat Polymerase DNA Directed Gamma 1 ELISA Kit
MBS069371-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Rat Polymerase DNA Directed Gamma 1 ELISA Kit
MBS069371-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Rat Polymerase DNA Directed Gamma 1 ELISA Kit
MBS069371-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Rat Polymerase DNA Directed Gamma 1 ELISA Kit
MBS069371-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
MBS2029756-001mg	MyBiosource	0.01mg	EUR 165

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
MBS2029756-005mg	MyBiosource	0.05mg	EUR 290

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
MBS2029756-01mg	MyBiosource	0.1mg	EUR 435

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
MBS2029756-02mg	MyBiosource	0.2mg	EUR 525

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
MBS2029756-05mg	MyBiosource	0.5mg	EUR 1005

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
RPF723Hu01	Cloud-Clone	10ug	EUR 164

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
4-RPF723Hu01	Cloud-Clone	Ask for price Ask for price Ask for price Ask for price Ask for price Ask for price Ask for price	5 mg 10ug 50ug 100 ug 200 ug 500 ug 1 mg
Description: Recombinant Human Polymerase DNA Directed Gamma 1 expressed in: E.coli

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
RPU51879-100ug	Biomatik Corporation	100ug	EUR 504.9

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
RPU51879-1mg	Biomatik Corporation	1mg	EUR 2238.6

Recombinant Polymerase DNA Directed Gamma 1 (POLg1)
RPU51879-50ug	Biomatik Corporation	50ug	EUR 405.9

Goat Polymerase DNA Directed Gamma 1 ELISA Kit
MBS106824-INQUIRE	MyBiosource	INQUIRE	Ask for price

Duck Polymerase DNA Directed Gamma 1 ELISA Kit
MBS069672-INQUIRE	MyBiosource	INQUIRE	Ask for price

Cavy Polymerase DNA Directed Gamma 1 ELISA Kit
MBS072214-INQUIRE	MyBiosource	INQUIRE	Ask for price

Fish Polymerase DNA Directed Gamma 1 ELISA Kit
MBS076413-INQUIRE	MyBiosource	INQUIRE	Ask for price

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx005134-100l	Abbexa	100 µl	EUR 400

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
20-abx005134	Abbexa	Ask for price Ask for price Ask for price Ask for price	20 ul 50 ul 100 ul 200 ul

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx005134-20l	Abbexa	20 µl	EUR 175

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx005134-50l	Abbexa	50 µl	EUR 275

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx031738-400l	Abbexa	400 µl	EUR 518.75

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx031738-400ul	Abbexa	400 ul	EUR 627.6

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx031738-80l	Abbexa	80 µl	EUR 250

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx036310-100g	Abbexa	100 µg	EUR 337.5

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx036310-100ug	Abbexa	100 ug	EUR 469.2

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx014427-100g	Abbexa	100 µg	EUR 43.75

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
20-abx014427	Abbexa	Ask for price Ask for price Ask for price Ask for price	10 ug 100 ug 200 ug 300 µg

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx114593-100l	Abbexa	100 µl	EUR 612.5

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
20-abx114593	Abbexa	Ask for price Ask for price	50 ul 150 ul

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx322945-100g	Abbexa	100 µg	EUR 250

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
20-abx322945	Abbexa	Ask for price Ask for price	50 ug 100 ug

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx322945-50g	Abbexa	50 µg	EUR 187.5

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx331384-100ul	Abbexa	100 ul	EUR 510

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx236611-100g	Abbexa	100 µg	EUR 350

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx236611-100ug	Abbexa	100 ug	EUR 577.2

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx311703-100g	Abbexa	100 µg	EUR 362.5

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
20-abx311703	Abbexa	Ask for price Ask for price Ask for price Ask for price Ask for price	20 ug 50 ug 100 ug 200 ug 1 mg

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx311703-20g	Abbexa	20 µg	EUR 162.5

Polymerase DNA Directed Gamma 2 (POLG2) Antibody
abx311703-50g	Abbexa	50 µg	EUR 250

Sheep Polymerase DNA Directed Gamma 1 ELISA Kit
MBS091924-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Sheep Polymerase DNA Directed Gamma 1 ELISA Kit
MBS091924-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Sheep Polymerase DNA Directed Gamma 1 ELISA Kit
MBS091924-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Sheep Polymerase DNA Directed Gamma 1 ELISA Kit
MBS091924-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Goose Polymerase DNA Directed Gamma 1 ELISA Kit
MBS074699-INQUIRE	MyBiosource	INQUIRE	Ask for price

Human Polymerase DNA Directed Gamma 1 ELISA Kit
MBS078803-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Human Polymerase DNA Directed Gamma 1 ELISA Kit
MBS078803-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Human Polymerase DNA Directed Gamma 1 ELISA Kit
MBS078803-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Human Polymerase DNA Directed Gamma 1 ELISA Kit
MBS078803-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Horse Polymerase DNA Directed Gamma 1 ELISA Kit
MBS065462-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Horse Polymerase DNA Directed Gamma 1 ELISA Kit
MBS065462-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Horse Polymerase DNA Directed Gamma 1 ELISA Kit
MBS065462-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Horse Polymerase DNA Directed Gamma 1 ELISA Kit
MBS065462-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Camel Polymerase DNA Directed Gamma 1 ELISA Kit
MBS061876-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Camel Polymerase DNA Directed Gamma 1 ELISA Kit
MBS061876-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Camel Polymerase DNA Directed Gamma 1 ELISA Kit
MBS061876-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Camel Polymerase DNA Directed Gamma 1 ELISA Kit
MBS061876-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Mouse Polymerase DNA Directed Gamma 1 ELISA Kit
MBS089783-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Mouse Polymerase DNA Directed Gamma 1 ELISA Kit
MBS089783-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Mouse Polymerase DNA Directed Gamma 1 ELISA Kit
MBS089783-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Mouse Polymerase DNA Directed Gamma 1 ELISA Kit
MBS089783-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Human Polymerase DNA Directed Gamma 1 ELISA Kit
IHUPOLG1KT	Innovative research	each	EUR 733
Description: Human Polymerase DNA Directed Gamma 1 ELISA Kit

Monkey Polymerase DNA Directed Gamma 1 ELISA Kit
MBS091839-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Monkey Polymerase DNA Directed Gamma 1 ELISA Kit
MBS091839-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Monkey Polymerase DNA Directed Gamma 1 ELISA Kit
MBS091839-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Monkey Polymerase DNA Directed Gamma 1 ELISA Kit
MBS091839-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Canine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS077277-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Canine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS077277-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Canine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS077277-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Canine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS077277-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Pigeon Polymerase DNA Directed Gamma 1 ELISA Kit
MBS060541-INQUIRE	MyBiosource	INQUIRE	Ask for price

Donkey Polymerase DNA Directed Gamma 1 ELISA Kit
MBS061826-INQUIRE	MyBiosource	INQUIRE	Ask for price

Bovine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS050779-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Bovine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS050779-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Bovine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS050779-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Bovine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS050779-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Rabbit Polymerase DNA Directed Gamma 1 ELISA Kit
MBS089005-INQUIRE	MyBiosource	INQUIRE	Ask for price

Chicken Polymerase DNA Directed Gamma 1 ELISA Kit
MBS093286-INQUIRE	MyBiosource	INQUIRE	Ask for price

Porcine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS047684-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Porcine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS047684-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Porcine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS047684-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Porcine Polymerase DNA Directed Gamma 1 ELISA Kit
MBS047684-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Hamster Polymerase DNA Directed Gamma 1 ELISA Kit
MBS087863-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 6725

Hamster Polymerase DNA Directed Gamma 1 ELISA Kit
MBS087863-48StripWells	MyBiosource	48-Strip-Wells	EUR 550

Hamster Polymerase DNA Directed Gamma 1 ELISA Kit
MBS087863-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 3420

Hamster Polymerase DNA Directed Gamma 1 ELISA Kit
MBS087863-96StripWells	MyBiosource	96-Strip-Wells	EUR 765

Polymerase DNA Directed Gamma 1 (POLg1) Polyclonal Antibody
CAU22415-100ul	Biomatik Corporation	100ul	EUR 235.2

Polymerase DNA Directed Gamma 1 (POLg1) Polyclonal Antibody
CAU22415-200ul	Biomatik Corporation	200ul	EUR 294

Human Polymerase DNA Directed Gamma 1 (POLg1) Protein
abx166623-100g	Abbexa	100 µg	EUR 537.5

Human Polymerase DNA Directed Gamma 1 (POLg1) Protein
20-abx166623	Abbexa	Ask for price Ask for price Ask for price Ask for price Ask for price	10 ug 50 ug 100 ug 200 ug 1 mg

Human Polymerase DNA Directed Gamma 1 (POLg1) Protein
abx166623-10g	Abbexa	10 µg	EUR 212.5

Human Polymerase DNA Directed Gamma 1 (POLg1) Protein
abx166623-50g	Abbexa	50 µg	EUR 375

Polymerase DNA Directed Gamma 2 (POLG2) Antibody (HRP)
abx311704-100g	Abbexa	100 µg	EUR 362.5

Polymerase DNA Directed Gamma 2 (POLG2) Antibody (HRP)
20-abx311704	Abbexa	Ask for price Ask for price Ask for price Ask for price Ask for price	20 ug 50 ug 100 ug 200 ug 1 mg

Polymerase DNA Directed Gamma 2 (POLG2) Antibody (HRP)
abx311704-20g	Abbexa	20 µg	EUR 162.5

Polymerase DNA Directed Gamma 2 (POLG2) Antibody (HRP)
abx311704-50g	Abbexa	50 µg	EUR 250

ELISA Kit for Polymerase DNA Directed Gamma 1 (POLg1)
SEF723Hu	Cloud-Clone	96Т	EUR 700

Polymerase DNA Directed Gamma 2 (POLG2) Antibody (FITC)
abx311705-100g	Abbexa	100 µg	EUR 362.5

Polymerase DNA Directed Gamma 2 (POLG2) Antibody (FITC)
20-abx311705	Abbexa	Ask for price Ask for price Ask for price Ask for price Ask for price	20 ug 50 ug 100 ug 200 ug 1 mg

Polymerase DNA Directed Gamma 2 (POLG2) Antibody (FITC)
abx311705-20g	Abbexa	20 µg	EUR 162.5

Polymerase DNA Directed Gamma 2 (POLG2) Antibody (FITC)
abx311705-50g	Abbexa	50 µg	EUR 250

Human Polymerase DNA Directed gamma 1 (POLg1) CLIA Kit
20-abx494991	Abbexa	Ask for price Ask for price Ask for price	96 tests 5 × 96 tests 10 × 96 tests

Human Polymerase DNA Directed gamma 1 (POLg1) ELISA Kit
20-abx152800	Abbexa	Ask for price Ask for price Ask for price	96 tests 5 × 96 tests 10 × 96 tests

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
DL-POLg1-Hu	DL Develop	96T	EUR 441
Description: tissue homogenates, cell lysates or other biological fluids.

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
DLR-POLg1-Hu	DL Develop	96T	EUR 463
Description: tissue homogenates, cell lysates or other biological fluids.

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
DLR-POLg1-Hu-48T	DL Develop	48T	EUR 620.4
Description: A sandwich quantitative ELISA assay kit for detection of Human Polymerase DNA Directed Gamma 1 (POLg1) in samples from tissue homogenates, cell lysates or other biological fluids.

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
DLR-POLg1-Hu-96T	DL Develop	96T	EUR 807.6
Description: A sandwich quantitative ELISA assay kit for detection of Human Polymerase DNA Directed Gamma 1 (POLg1) in samples from tissue homogenates, cell lysates or other biological fluids.

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
EKU06740-48T	Biomatik Corporation	48T	EUR 555.66

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
EKU06740-5x96T	Biomatik Corporation	5x96T	EUR 3770.55

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
EKU06740-96T	Biomatik Corporation	96T	EUR 793.8

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
EK16193	SAB	96Т	EUR 768

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
EKN47851-48T	Biomatik Corporation	48T	EUR 378.7

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
EKN47851-5x96T	Biomatik Corporation	5x96T	EUR 2569.75

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
EKN47851-96T	Biomatik Corporation	96T	EUR 541

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS4501953-10x96Tests	MyBiosource	10x96Tests	EUR 5260

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS4501953-48Tests	MyBiosource	48Tests	EUR 460

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS4501953-5x96Tests	MyBiosource	5x96Tests	EUR 2700

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS4501953-96Test	MyBiosource	96Test	EUR 605

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS2022618-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 5320

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS2022618-24StripWells	MyBiosource	24-Strip-Wells	EUR 360

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS2022618-48StripWells	MyBiosource	48-Strip-Wells	EUR 545

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS2022618-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 2915

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS2022618-96StripWells	MyBiosource	96-Strip-Wells	EUR 720

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS453428-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 5050

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS453428-48StripWells	MyBiosource	48-Strip-Wells	EUR 440

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS453428-5x96StripWells	MyBiosource	5x96-Strip-Wells	EUR 2590

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS453428-96StripWells	MyBiosource	96-Strip-Wells	EUR 585

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS2705897-10x96StripWells	MyBiosource	10x96-Strip-Wells	EUR 3130

Human Polymerase DNA Directed Gamma 1 (POLg1) ELISA Kit
MBS2705897-24StripWells	MyBiosource	24-Strip-Wells	EUR 255

All additional binding capacity on the nitrocellulose was blocked with excess protein; then a specific antibody was bound and, finally, a second antibody directed against the first antibody. The second antibody was either radioactively labeled or conjugated to fluorescein or to peroxidase. The specific protein was then detected by either autoradiography, under UV light, or by the peroxidase reaction product, respectively. In the latter case, as little as 100 pg of protein was clearly detectable. It is anticipated that the procedure will be applicable to analysis of a wide variety of proteins with specific reactions or ligands.

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB.

MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

The CCP4 (Collaborative Computational Project, number 4) program suite is a collection of programs and associated data and subroutine libraries which can be used for macromolecular structure determination by X-ray crystallography. The suite is designed to be flexible, allowing users a number of methods of achieving their aims and so there may be more than one program to cover each function. The programs are written mainly in standard Fortran77. They are from a wide variety of sources but are connected by standard data file formats. The package has been ported to all the major platforms under both Unix and VMS. The suite is distributed by anonymous ftp from Daresbury Laboratory and is widely used throughout the world.

VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more “representations,” in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms.

The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback.

High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation.

VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.